Lost Son
by RavenousWolfBoy
Summary: What If at the same time as the Kyuubi attack Iwa had decided to get revenge on the Yondaime. How would one act of vengeance completely change the Shinobi world, or would it? T for violence if I decide to follow through on later chapters. No pairings
1. Prologue

__**A/N: So first story r&r please. also I don't own Naruto and while I usually love it don't think I could handle that responsibility.**

_Amegakure_

The Chamber was dark and cavernous located in the highest tower of the hidden village. In it was a desk with a various stacks of paper in severe disarray laid upon it. Also in the room was a statue with an aura of darkness surrounding it. Attached to the statue was a man with several black rods protruding from his back, his short red hair hung concealing most of his face save one eye, an eye whose pattern was oddly reminiscent of a rippling pond. All of sudden without any noise there was a man wearing a mask. The mask had a pattern of dark clouds swirling from the center which just happened to be the man's right eye. This man's eye was strange as well similar to that of a three pronged pinwheel.

"What Happened?" The red haired man asked

"The Yondaime proved more persistent than expected." The Masked man responded grimly

"I'm assuming you were unable to retrieve the Kyuubi."

"Unfortunately…" His silence became foreboding.

"So where do we go from here."

"I have a few personal matters that need to be taken care of. So in the meanwhile I'm going to need you to rebuild your little organization," he dropped one of folders at the feet of the Man attached to the Statue completely ignoring the desk.

"What's this?"

"Somehow I doubt that you and your paper doll will be able to collect all nine of the Bijuu by yourself, six paths or no. They're dossier of several powerful rogue ninja who may be amenable to our goals." The masked man turned as if to leave

"And what If they're not"

"…Persuade them" with that the man disappeared as if he was never there.

_Konohagakure- _

In the Hokage's chambers were two men. The first was standing, he had long spiky white hair, was rather tall and slightly pudgy with the air of one who really never aged beyond 13 despite his many wrinkles which hinted at an advanced age. The second of the two men was sitting down behind a desk his hair was also spiky but where the older man's hair was white from birth or age the younger mans was pure gold. In further contrast the younger man seemed to hold the weight of the world on his shoulders and seemed almost as if he was ready to break. He looked up at the older man and with a voice raw with emotion he spoke.

"Jiraiya-Sensei, please tell me you have something good to tell me. After today I just…don't think I can take anymore" Almost immediately Jiraiya's buoyancy reduced dramatically and he began to look critically at his former pupil.

"What's wrong Minato?" For a brief moment Minato's eyes glazed over lost in the remembrance of the day's events.

"It all went straight to hell sensei. The Kyuubi was set free."

"Minato I'm so sorry how's Kushina is she all right?" The younger man's shoulders sagged and he began weeping as if the world itself had collapsed.

"She's gone," He whispered "Kushina's dead, and I couldn't save her."

"Oh Minato," Jiraiya walked over to embrace his former pupil. "It's okay I know you did everything you could."

"But that's just it, I'm the Hokage. How am I supposed to be able to protect an entire village if I can't even defend my own family?"

"Your family?" Jiraiya's tone became more insistent "Minato how's the baby, is it alright"

"No," Minato sighed tears still streaming down his face "My child's been kidnapped I don't where to yet I've put the Tsume's clan on his trail but I haven't heard anything back yet."

"Minato how could something like this even happen" The news of the loss shocking the normally unflappable ninja.

"I don't know do you think I wanted things to turn out this way" Minato barely stopped himself from shouting.

"No. No!" Jiraiya attempted to reassure Minato and sighed. "Just start from the Beginning okay." It took Minato a few seconds to completely pull himself together and begin to speak. Jiraiya noted the deep circles surrounding the Hokage's eyes.

"Today was the day. Everyone knew that our son would be born. Kushina was so scared of the childbirth. The council said that in order to protect the village, the actual birth needed to take place outside of the village inside of a sealed barrier. Everything was going fine until he showed up. He used some sort of dimensional jutsu to get inside of the barrier and somehow he got hold of my child. I had to get hold of my child so I used my …. Jutsu to get my child away from him, but that just left Kushina alone with him. He ripped the Kyuubi out of her, and by the time I got back it was too late. She was already on her way to death. I brought her to my child so she could have some peace and kept going to try and seal the Kyuubi before it was too late. It was then I failed Konoha again. While I was able to break the masked man's control of the Kyuubi I couldn't stop the Kyuubi from rampaging into the town. I knew that in a few years it wouldn't matter if I killed the Kyuubi because even if I could the Kyuubi would just reform and we'd be going through this all over again. So, I'd decided to seal it." At this the Yondaime stopped speaking his gaze downcast he seemed lost in thought, scared and a little ashamed. Jiraiya frustrated began to shake the Hokage a little.

"Who did you seal the Kyuubi into?" Minato looked up at Jiraiya emotions dancing across his face until finally he seemed to resolve himself.

"I'm sorry Sensei I can't tell you that."

"Why Not?!"

"No one knows and the Sandaime made me promise to keep it that way for now"

"Sarutobi, why would he say something like that?"

"The Sandaime believed that the best way to keep the jinchuuriki safe was if we made sure that no one who exactly he or she was and while I don't agree with it I thought it would be best to respect his last request."

"His last request… Sensei is dead?"

"I'm sorry Jiraiya when I was about to perform the Shiki Fuin in order to seal the Kyuubi he took my place" Jiraiya struggled for a moment then his face went devoid of emotion.

"It's not your fault Minato, sensei chose this and if he said to keep the identity of the Jinchuuriki then of course you can't go against his wishes. I just wish…"

"I know Sensei."

"So what's the damage to the town?"

"One of the walls was breached and we had about 50 casualties 43 of which were shinobi. We had 16 Shinobi deaths and 2 civilians as well."

"So, 18 dead altogether." Jiraiya sighed shaking his head at the needless loss of life. "Well I wish I was the bearer of good news but we're not so lucky"

"Why what happened"

"Nothing conclusive but the 'Rice Paddy' village seems to be moving past their internal conflicts due to a mysterious savior. There's talk of him developing a hidden village there"

"Really?" Despite the current problems of his village the 4th new the importance of Jiraiya's reports and relied on his Shinobi training to process the information. "What course of action do you recommend?"

"To be honest I haven't been able discern anything too sinister and we do still have to worry about threats from Iwa especially now that our infrastructure has been wrecked by the threat of the Kyuubi. Along those lines now would be the perfect time for enemy spies and shinobi to infiltrate Konoha leaving us vulnerable to attack in the coming years."

"I see" Minato rubbed his forehead and took a few minutes to think. "In that case your orders are simple. Stay here, find, and train a successor." At this Jiraiya visibly blanched.

"Minato be reasonable it's unlikely that I'll find someone that the toads will accept quickly enough for me to continue my operations, and if I were to stop operations now it would take years to build it back up again."

"Jiraiya sensei, you're misunderstanding. I don't want you to find another toad sage. I want you to find another spymaster. If you could train more spies as well that would be great."

"I see, however even so, the time it would take me to find an apprentice would still make it harder for me to continue at what I do best. " Jiraiya said this last bit with an overly provocative grin. Minato just smiled amused by the antics of his former sensei.

"Jiraiya, I'm sorry and while I do appreciate your efforts in defusing foreign threats, I'm beginning to think that in the coming years we're going to need to focus more on counterintelligence. The masked man who awakened the Kyuubi knew the exact time and place of Kushina's pregnancy. Things he would only know if he had someone in Konoha feeding him information. You said it yourself its likely we'll have an influx of enemy ninja's infiltrate Konoha. Furthermore with Konoha weakened as it is it couldn't hurt to have one of our most powerful shinobi here as we rebuild." Minato knew he was laying it on a bit thick but he knew that his Sensei could be a little bit too stubborn unless bombarded physically or in this case mentally. "Jiraiya please the village needs you for a multitude of reasons that I can't even begin to go into right now." Jiraiya just sighed.

"Not to mention the fact that I'm old right." He waved his hands when he saw Minato try to interrupt and smirked. "Don't even try it, I've known you for quite a while and it would take 100 years for you to be able to deceive me. You're afraid of me dying out there like the Third Hokage aren't you? You're forgetting that I've been able to take care of myself for quite a while now. Don't worry about me though because you're right. Not about the whole trying to protect me thing because Hokage or not I won't let even you protect me from my own choices. I am Jiraiya of the Sannin after all. However, what you said before about enemy spies was probably true so …I'll stay. With that he gave a tremendous grin that traveled from ear to ear. Minato couldn't help but give a soft chuckle at the Toad Sage.

"Well, great I'll get you set up with an office at ANBU Headquar-"

"Whoa an office" Almost immediately Jiraiya began shaking his head "Sorry Minato no can do, an office means infrastructure and infrastructure means infiltration" Minato nodded slowly adjusting to a completely new way of thinking.

"So what will you need?"

"Full access to all your files secret or not and ability to question and recruit anyone I want civilian or shinobi."

"Civilians, Jiraiya are you sure…" Minato began.

"Trust me, Minato you'll be surprised at how much of my information comes from people who are supposed to know nothing" Minato just closed his eyes in resignation. "Anyways I gotta go see ya' in about a year kid."

"Wait, a year?"

"Come on Minato, as much as I love this village, I need to tie up a few loose ends up before I comeback.

"I understand, but Jiraiya just make sure you come back okay?" Jiraiya gave him a trademark smile and replied

"Of course, and two pieces of advice to you kid, the best way to keep a secret is to tell absolutely no one." At this Minato visibly flinched before dispelling into a cloud of smoke the signature of the Shadow Clone. The 4th Hokage leaned back in his chair and planned for the future.

The sound of wailing permeated throughout the forest. A newborn baby wrapped in orange swaddling cried out in hunger in the bare arm of a man. The man wore all black shinobi gear that with metal gauntlets and mesh armor around his ankles. His face was covered with black and red wrappings that were overlaid by a hitai-ite with the symbol Iwagakure crossed out. While his left arm carried the child his right hand was holding his right side. The man limped through the forest leaning heavily on the trees he walked by.

"Shut up Brat, or else I'll kill you just like I killed your mother." He snarled weakly before falling to the ground. "Shit." He brought his hand from his side to in front of his face. The metal encased appendage was covered in blood.

Well I guess it doesn't matter now" he muttered as he reached down towards his side pulling out the kunai that he had originally kept in. Blood flowed freely from his side and the ninja knew he was reaching his final moments. The ninja reversed his grip on the kunai and brought it up to the throat of the infant. 'I guess all that's left is too make the Hokage pay.'

Blood flowed as a cry pierced the forest.


	2. Meet Genji

**Disclaimer: I don't own Naruto cause I don't have a couple billion dollars**

_4 years later: Ranzuendo no Mura ,Yu No Kuni_

IT was Dark at first. Warm. Safe. Then his world was turned upside down. It was an upheaval kind of like a constant churning. To be honest he wasn't really sure what it was. All he knew was it hurt. The pain was without question the worst thing he had felt in his entire life. Just when he thought it couldn't get any worse he felt it, a pure and almost animal hatred bent on destroying absolutely everything in its path. The only redeeming feature of the turmoil that his life had become was the mere fact that he somehow knew that whatever the anger was, either didn't know or didn't care that he was there and left him alone. It was a small comfort when the only options were between absolute annihilation and unending pain, but it was a comfort all the same.

After what seemed like an eternity the pain and the churning stopped. It was still dark but colder and more dangerous. He opened his eyes and was almost immediately blinded from the transition into the light. When his eyes finally began to adjust to the light and he could see his surroundings, he found himself staring into the face of a man in a mask of swirling colors.

* * *

A young boy woke up with a shout. His clear blue eyes dilated despite the darkness of his room. His hair slick with sweat covered his face that was marked by three lines on either side, like whiskers. He gasped for air, the dream had been the most vivid and intense thing he had ever experienced. He brought his hands to his face, noticing both his hands and face were drenched in sweat. He heard footsteps approaching his room before barging in. The man who entered the small bedroom was tall well over 6 ft. His hair was pitch black and short cropped. He was well muscled with interlocking scars traversing up his arms. He wore no shirt and a … that covered the lower regions of his body. The man moved quickly to the side of the frightened young boy. The man said nothing content to wrap up the child in his arms and calm him with his presence.

"Tou-san?" Despite the darkness the boy fixed his gaze to the stronger man "the dream, it was the same one"

"Don't worry Genji, we'll fix it." The man spoke calmly and deliberately and stayed with his son until he fell asleep.

* * *

The next day Genji's father, Takeda, sent him out to play with the other children. Although Genji loved the smithy and would eventually take it over Takeda believed it to be too dangerous for Genji at four to be around the white hot fires of the forge. On the other hand the children of the village were all watched over by the collective of village mothers and despite they're constant nagging and prying into his business Takeda knew that his son would be safe with them.

It could be said that Takeda had €problems with the females of the village. Well it was really one problem. Takeda was single and had no intentions of getting married never had and from all perspectives never would. It wasn't that Takeda had a problem with marriage or even women in general and it wasn't that he had set his eyes on any of the young men in the village. Takeda simply didn't particularly enjoy the company of people. And it wasn't until he had his son that Takeda was able to enter into an unspoken truce with the rest of the villagers.

As Takeda worked on re-forging an axe, he began thinking on the troubles of his son. The nightmares had started a year ago when Genji turned three and they were always the same. Neither the village priestess nor herbalist could figure out exactly what was wrong with the boy and could prescribe no cure for him. A few hours later when Takeda had finished he knew what he had to do. He had known all along but he really hated asking for help. Takeda tidied up his workbench taking off his blacksmiths cap and apron as he did. He then put on a dark blue kimono and matching hakama before coming upon an ornate cylindrical object that was about 10 inches long. He debated briefly before putting the object in the sleeve of his Kimono and moving on to lock up the smithy.

Takeda then proceeded walked to the outskirts of the village until he reached a little cabin that was right on the edge of the forest and knocked. Ten minutes later after waiting patiently Takeda was rewarded with the sight of a man coming out of the forest. The man was of average height with short salt and pepper hair. He wore a grey hooded coat along with faded green pants and wore sunglasses over his eyes.

"Takeda"

"Satoshi"

"Did you need something" The man asked quietly. Takeda merely grunted his assent. "Alright well come on in" With that the man opened the door of the cabin and walked in followed closely by the silent blacksmith who ducked in order to save his forehead. Inside there was a small bed a table and two chairs.

"Have a seat, so tell me what's wrong, and use your words this time" A smile tugging at the shorter man's lips.

"Genji has a nightmare." Takeda said shortly. Takeda was a man of few words and if possible none, saying only what he thought to be absolutely necessary to get his point across. Sometimes a little deciphering had to be done on the part of the listener.

"Really, how long has he had them?"

"Not them…**IT**…and a year."

"So Genji has had the same nightmare for the last year? What's the dream about" Takeda gave the hooded man a flat stare as if working out whether he was joking or not and then recounted the entirety of the dream him. After the dream was told there was silence in the cabin as Satoshi thought on the disturbing nature of the dream.

"It's definitely interesting but what do you want me to do about it?" Takeda's face twisted as if what he was about to say left a bad taste in his mouth.

"I know what you are" Satoshi gave a slight grin

"Oh really, I'm going to assume you don't mean an exceptional hunter and tracker"

"No,"

"Okay then I'll bite what am I?"

"A Nuke-Nin" As if those words were the sound of a starter gun Satoshi leapt into action disappearing into a cloud of smoke and reappearing behind Takeda, a kunai to the blacksmiths throat. Takeda's face could have been made out of granite. "It would be the last thing you ever did" as he said this Satoshi felt something poke his left side and he looked down. The tip of an impossibly sharp tanto rested right where his kidney was, its sheath fell to the ground from Takeda's sleeve.

"Do you really think you'd really be fast enough?"

"I do" After a few tense moments Satoshi once again disappeared and reappeared in the seat as if he had never left. A small chuckle left his lips

"Well that explains some things. I'm assuming you came by to see if I knew some genjutsu to keep the nightmares at bay." Takeda nodded. "Well, unfortunately I don't, but bring him by next week and I'll see if I can do anything for him." Once again Takeda nodded and having completed what he had set out to do he gathered his sheath slipping the tanto back up his sleeve and made to leave saying little in way of farewell. After he left Satoshi chuckled again while he took off his shades. Perfectly white eyes with no pupils or irises shone forth. 'Well this is bound to be interesting' he thought before whispering the word "_Byakugan" _The veins around his eyes bulged out, and thin iris's became visible. Instantly the layout of the world was transformed into a panorama of his surroundings. Satoshi focused his gaze on the departing Blacksmith and began to ruminate.

* * *

Genji had a dream. He wanted to be the best blacksmith in the world just like his dad. In all honesty Genji wanted to do a lot of things just like his dad, like wear funny clothes and sit very still without moving, but Genji was too small to wear the weird robes of his father and well he had never been very good at sitting still so all that was left was becoming a blacksmith. While he was still too young to actually use the forge every night after dinner his Tou-san would teach him something new about the different types of metals and ores, different methods of repairing items and if he got really lucky how to forge swords. On the nights where they talked about swords Takeda would go on and on until finally he would realize how late it was and bring him to bed. Genji loved it when Tou-san would talk about swords because when he did his father's voice became almost tender and spoke in long flowing sentences that seemed like they would never end. Genji knew his father didn't like talking much and so always felt lucky whenever he got a paragraph or two out of father. He never really understood why some of the bigger kids in the village called his father "The Demon Blacksmith" after all Tou-san wasn't at all loud and scary like a demon. So when Takeda told him that he had found a way to fix his nightmare's he trusted him implicitly. He trusted him that is up until the point he met the man with white eyes then he began to wonder if his father wasn't a little crazy.

"Hello, Genji my name's Satoshi" the white-eyed man had a nice quiet smile that slightly crinkled up the corners of his eyes upward.

"Hello," Genji began tapping his feet softly and rapidly. He looked up at his father who chose to stand, instead of sit, behind him. Takeda gave him a small smile and put his hand on his son's shoulder. The tapping of Genji's feet stopped. The drumming of his hands on the table however began. Satoshi's smile widen even further.

"Genji, I know there are probably a million questions that you want to ask me so I want you to feel free and say whatever is on your mind okay." Genji's blue eyes widened but he stayed quiet. The drumming became louder and faster. 'Let's try something else' Satoshi thought before concentrating on his left hand.

"Genji, do you see my hand" The blonde looked down to see the hands of the older man and was shocked to see one of them cover in a turquoise aura. Finally the energetic boy could hold it in no longer.

"What is that blue stuff? Is your hand on fire? Does it hurt? Tou-san said I can't use the forge cause it'll burn me, but you're on fire and you're not burning. Is that why Tou-san is allowed to use the forge and I'm not? Do you have a forge too? Do all grownups do that?" Genji spoke like a runaway train following every question with either another question or another sentence and he didn't stop until he ran out of breath. "Can you teach me how to do that so I can use the forge? Why is it blue? Tou-san says blue fire is the coldest fire there is that's why I wear blue. I hate blue. I can't wait till he lets me wear red cause red is hotter than blue."

"Genji," Takeda's voice wasn't loud or harsh just stern, an obvious command.

"No it's okay Takeda don't worry so much I'm beginning to get an idea of what's going on his head at the very least. Honestly after talking to you it's refreshing to hear him speak." Satoshi directed his attention to the whiskered boy with another grin. "Alright, so let's do everyone a favor, you can ask me three questions so you don't explode and you won't get in trouble with your Tou-san okay. Although this time when you ask a question, wait for me to answer. Alright?" Naruto nodded and scrunched up his face so hard it looked like he hurt himself.

"What is that stuff on your hand"

"This is called Chakra; it's a type of energy that is inside of everything. It's made up of the natural energy of your body and spirit. If you concentrate it you can control it a little to appear outside of your body, and if focus really, really hard you can make it do anything you want it to." The boys blue eyes widened as he considered this.

"Can I use it to make a sword?"

"Well you would have to ask your Tou-san but I don't see why not. Actually there are several special weapons in the world that use chakra to activate there special abilities." Genji gave a toothy grin and laughed

"That's awesome, I'll learn how to use that blue stuff and then I'll become a better than even you Tou-san!" Takeda merely smiled at his son.

"I bet you will Genji. Now you have one more question left. Use it wisely." Once again Genji scrunched up his face and Satoshi couldn't help but think of it as his 'thinking pose'.

"Will you make my nightmares go away?" Genji's cerulean eyes locked on to the alabaster orbs of Satoshi and held them. His face was solemn almost a perfect mimicry of his father's typical impassiveness.

"Yes Genji, I will."

* * *

After their session Takeda told his son to wait outside the cabin that was the nuke-nin's home. Takeda turned towards the now weary Satoshi as he put his shades back on.

"Can you help him?" Satoshi just shrugged.

"I don't know I was unable to ascertain the reason for his nightmare from the questions I asked him. I really would rather not use any genjutsu on him for two reasons. Who knows how that might damage the psyche of a child his age it might scar him for life. Furthermore using genjutsu wouldn't solve the real problem."

"What real problem?"

"Honestly, I don't know. It's not as if he's actually scared of anything, but he's having these dreams for a reason and using genjutsu would just treat the symptom not the cause." Takeda took a moment to compose himself at hearing the diagnosis.

"What do I do?" The blacksmith asked.

"I don't know, tire him out." Takeda grunted something that probably meant 'What the hell are you talking about?' Satoshi looked up at him an almost excited glint in his eyes.

"You haven't noticed? He didn't stop moving once when I had him in here. I bet its absolute hell trying to get him to bed. The kid is literally a ball of energy and I mean that. When I used the Byakugan during the session on him you wouldn't believe it. The kid is a mass of chakra."

"So?"

"So, chakra is physical energy, produced by the activity of cells in our bodies, which has been enriched by our spiritual energy, produced by our life experiences otherwise known as willpower. I'm sure that all that chakra is just more fuel to the fire of his subconscious mind. It's a wonder he doesn't explode when he tries to sit still. I'm betting it's pretty hard for him concentrate on anything." Takeda frowned at that.

"He concentrates."

"On what you say I wouldn't doubt it, but how about when other people try to teach him something" Takeda remembered a particular instance when one of the village housewives had tried to teach the children how to count. His son had come home dirty, bleeding and grinning without a clue that three followed four until Takeda sat him down himself.

"What do I do?"

"Well if you don't mind I could start teaching him." Takeda's gaze was stormy. "Hold on, I'm not going to teach him how to use any ninjutsu but I think teaching him some chakra control would go along away in at least calming him down, and when I'm done with him I would recommend you take him and start disciplining his mind."

"He's too young." Satoshi narrowed his eyes at Takeda's rebuttal.

"Really or is it you just don't want him associating with a Shinobi you samurai dog…" A wakizashi sliced the air where Satoshi's head had been. The shinobi bent slightly avoiding the blade of the short sword if just barely. Satoshi gave him a satisfied smirk. Takeda had already sheathed his weapon in the folds of his robe. He gave a simple shrug as if to say 'Now we're even' and turned to leave. When he reached the door he stopped.

"Fine, but no ninjutsu not unless I say so."

**A/N: So yes Genji is Naruto, and Takeda is a Samurai, and Satoshi is a Hyuuga. I'll do a couple flashbacks to explain how they all three met, and for those of you too lazy to look up the words in japanese (I know I would be):**

**1. Yu no Kuni = Land of Whirlpools**

**2. Ranzuendo no Mura = The Cape Village**

**3. Hakama = a traditional Japanese lower region covering worn by Samurai back in the day**

**4. Tanto = Really short single edge blade for stabbing and cutting**

**5. Wakizashi = Japanese short sword used in tandem with the Katana**

**KK that's all next up we go back to Konoha.**


End file.
